Moreover, Barcelona's performance this season has been less stable compared to Atletico, but now everything has changed and the additional 3 points have put Barcelona in second place in the standings. I think Atletico must know that all teams are the same and must try to win and not just focus too much on their local rivals like Real Madrid. The additional 3 points are important to maintain stability and also create a safe position in top competition. 
I thought Atletico Madrid could make things difficult for Barcelona, but I was wrong. In fact I think like you, because they concede the ball too easily and it looks weak like in your picture. It seems Madrid have to learn a lot from Barcelona so they can make Atletico like a docile cat. It seems that Jao Felix became Barcelona's differentiating actor, with his anger he worked hard to make Simeone feel guilty about letting go.
Perhaps, Barcelona win wasn't a surprise either but what was a surprise was the final score, because Barcelona managed to get big win with a clean sheet of 0-3. Obviously, a defeat with a score like this is a bad result for Atletico which team playing at home. But yes, with Barcelona success this is certainly a decent position for Barcelona to be able to finish in second place.
To be frank we all were expecting Barcelona to win since they had been in a good form lately while Atletico has been really inconsistent but at least thought the match would be challenging which wasn't quite so. Barcelona probably will finish second, Girona as not really been having a great game lately.
But for Atletico, of course Atletico still have to work well again if Atletico want to return to the top four, because Bilbao at this moment is also a very good team. Therefore, it is likely to be difficult for Atletico to return to the top four even though indeed, Bilbao and Atletico only have a gap of 1 point but yes, because this moment Atletico are experiencing performance instability, it will certainly be difficult for Atletico to overtake Bilbao.
I think Atletico Madrid still has high chances of Making top 4 all they need is for Athletic club to lose or draw a match while they are just consistent and take their chances well don't forget we saw similar situations with Arsenal earlier this which made us write them off as league contenders but surprisingly they are doing great now and it's a three horse race to get the epl title.